Genetic diversity of Nile tilapia (Oreochromis niloticus, L. 1758) in native and introduced populations in East Africa


  • Charles Twesigye Kakuhikire Kyambogo University
  • Francis W. Nsubuga Department of Geography, Kyambogo University, Kampala, Uganda
  • Richard Raja Department of Biological Sciences, Kyambogo University, Kampala, Uganda
  • Paul Kato Department of Biological Sciences, Faculty of Science, Kyambogo University, P.O. Box 1, Kyambogo, Kampala, Uganda



Aquaculture, Cage farming,, Gene flow,, Nile tilapia,, overfishing


Freshwater fish in East African Lakes are under severe threat due to the recently discovered oil and gas in the Albertine Region and overfishing across the entire East African Region. The threats, primarily caused by overfishing, are a matter of declining fish populations and a potential reduction in genetic diversity in the surviving populations due to genetic drift. This study, therefore, is of utmost importance as it assessed genetic diversity in seven populations, including five from native and two from introduced populations. The assessment of genetic diversity in Oreochromis niloticus was conducted using molecular markers in 128 samples. The results showed a moderate genetic variation between native and introduced populations at mitochondrial and microsatellite loci. The potential effects of overfishing, fish introductions, and new threats from cage farming on the genetic diversity and ecological integrity of wildlife species are discussed, highlighting the need for immediate action.

 Keywords: Aquaculture, Cage farming, Gene flow, Nile tilapia, overfishing


Allen, B.E.; Bowles, E.; Morris, M.R.J.; Rogers, S.M. (2018). Loss of SNP genetic diversity following population collapse in a recreational walleye (Sander vitreus) fishery. Canadian Journal of Fisheries and Aquatic Sciences, 75, 1644–1651.

Allendorf, F.W. ( 2017). Genetics and the conservation of natural populations: Allozymes to genomes. Molecular Ecolology, 2017, 26, 420–430.

Allendorf FW, England PR, Luikart G, Ritchie PA, Ryman N.(2008). Genetic effects of harvest on wild animal populations. Trends Ecol Evol. 2008;23 (6):327–37

Agnèse J-F, Adépo-Gourène B, Abban EK, Fermon Y.(1997). Genetic differentiation among natural populations of the Nile tilapia Oreochromis niloticus (Teleostei, Cichlidae). Heredity. 1997; 79 (1):88–96.

Arthington, A.H.; Dulvy, N.K.; Gladstone, W.; Winfield, I.J.(2016). Fish conservation in freshwater and marine realms: Status, threats and management. Aquatic Conservation: Marine and Freshwater Ecosystems, 2016, 26, 838–857.

Balirwa JS.(1992). The evolution of the fishery of Oreochromis niloticus (Pisces: Cichlidae) in Lake Victoria. Hydrobiologia. 1992; 232 (1):85–9

Beadle, L. C.(1981). The Inland Waters of Tropical Africa. London: Longman.

Brichard, L.C. (1989). Pierre Brichard’s book of cichlids and all the other fishes of Lake Tanganyika. TFH Publications, Neptune City.

Dawson, M.N.(2012). Species richness, habitable volume, and species densities in freshwater, the sea, and on land. Front. Biogeogr. 2012, 4, 105–116.

D’Aloia, C.C.; Andrés, J.A.; Bogdanowicz, S.M.; McCune, A.R.; Harrison, R.G.; Buston, P.M. (2020). Unraveling hierarchical genetic structure in a marine metapopulation: A comparison of three high-thr oughput genotyping approaches. Molecular Ecology, 2020, 29, 2189–2203.

Darwall, W.R.T., Smith, K.G., Allen, D.J., Holland, R.A., Harrison, I.J. and Brooks, E.G.E. (2011). The diversity of life in African freshwaters: underwater, under threat. Gland, Switzerland nd Cambridge, UK: IUCN

Dumont H.J. (2009). The Nile: Origin, environments, limnology, and human use: Springer Science & Business Media; 2009.

Excoffier, L., Smouse, P. and Quattro, J. (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics, 131, 479-491

FAO. (2020). The State of World Fisheries and Aquaculture 2020; Sustainability in Action; FAO: Rome, Italy, 2020.

Fryer, G. & Iles, T. D. (1972). The Cichlid Fishes of the Great Lakes of Africa: Their Biology and Evolution. J Oliver and Boyd, Edinburgh.

Greenwood, P.H. (1983). ‘The zoogeography of African Freshwater fishes: Bioaccountancy or Biogeography?’. In: R.W. Sims, J.H. Price and P.E.S. Whalley (eds.) Evolution, Time and Space: The Emergence of the Biosphere, Systematics Association Special Volume. pp. 179–199. London, UK and New York, USA: Academic Press.

Hecky, R.E., Mugidde, R., Ramlal, P.S., Talbot, M.R. & Kling, G.W. (2010). ‘Multiple stressors cause rapid ecosystem change in Lake Victoria’. Freshwater Biology. 55:19–42.

Johnson, T.C. Scholz,C.A , &Talbot, M.R.(1996). Late Pleistocene desiccation of Lake Victoria and rapid evolution of cichlid fishes,” Science, vol. 273, no. 5278, pp. 1091–1093, 1996.

Kaufman L. (1992). Catastrophic change in species-rich freshwater ecosystems. BioScience. 1992; 42(11):846–58.

Kocher, T. (2004). Adaptive evolution and explosive speciation: The cichlid fish model. Nature reviews. Genetics. 5. 288–98. 10.1038/nrg1316.

Lee, W.J. and Kocher,T.D. (1996). Microsatellite DNA Markers for Genetic Mapping in the Oreochromis niloticus. Journal of Fish, 49, 169-171Nei, M. 1987. Molecular

Evolutionary Genetics. Columbia University Press, New York.

Lemopoulos, A.; Prokkola, J.M.; Uusi-Heikkilä, S.; Vasemägi, A.; Huusko, A.; Hyvärinen, P.; Koljonen, M.-L.; Koskiniemi, J.; Vainikka, A.(2019) Comparing RADseq and microsatellites for estimating genetic diversity and relatedness—Implications for brown trout conservation. Ecol. Evol. 2019, 9, 2106–2120

Lubembe SI, Walumona JR, Hyangya BL, Kondowe BN, Kulimushi J-DM, Shamamba GA, Kulimushi AM, Hounsounou BHR, Mbalassa M, Masese FO and Masilya MP (2024). Environmental impacts of tilapia fish cage aquaculture on water physico-chemical parameters of Lake Kivu, Democratic Republic of the Congo. Front. Water 6:1325967. doi: 10.3389/frwa.2024.1325967

Meier, J.I., Marques, D.A., Mwaiko, S., Wagner, C.E., Excoffier, L. and Seehausen, O. (2017). Ancient hybridization fuels rapid cichlid fish adaptive radiations. Nature Communications. ncomms14363

Mwanja, W.W. (1996). Genetic Variability and Population Structure ofTilapiine Fauna of Lake Victoria Basin (Uganda) in Relation to Exotic Species Introductions Nei, M. (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.

Njiru, M., Nyamweya, C., Gichuki, J., Mugidde, R., Mkumbo, O. and Witte, F. (2012). ‘Increase in Anoxia in Lake Victoria and Its Effects on the Fishery’. In: P. Padilla (ed.) Anoxia. pp. 99-128. InTech.

Ogutu-Ohwayo, R. (1990). The decline of the native fishes of lakes Victoria and Kyoga (East Africa) and the impact of introduced species, especially the Nile perch, Lates niloticus, and the Nile tilapia, Oreochromis niloticus. Environmental Biology of Fishes, 27(2):81-96

Pinsky, M.L.; Palumbi, S.R. Meta-analysis reveals lower genetic diversity in overfished populations. Molecular Ecolology (2014), 23, 29–39.

Okechi, J.K, Nick Peoples, N. Sangara, C.N., Sarah Glaser, S., Leslie Kaufman, L. (2022). The ecological health of Lake Victoria (Kenya) in the face of growing cage aquaculture. Conservation Science and Practice. 2022;4:e12826

Rhymer J.M., Simberloff D. Extinction by hybridization and introgression. Annual Review of Ecological Systems, 1996; 27(1):83–109.

Righi, T.; Splendiani, A.; Fioravanti, T.; Casoni, E.; Gioacchini, G.; Carnevali, O.; Caputo Barucchi, V.(2020) Loss of mitochondrial genetic diversity in overexploited Mediterranean swordfish (Xiphias gladius, 1759) population. Diversity2020, 12, 170.

Roberts, T.R. (1975). ‘Geographical distribution of African freshwater fishes’. Zoological Journal of the Linnean Society. 57:249–319.

Snoeks, J.(1994). The haplochromines (Teleostei, Cichlidae) of Lake Kivu (East Africa): a

taxonomic revision with notes on their ecology. Tervuren, Belgium : Koninklijk Museum voor


Sadler, D.E., Watts, P.C., Uusi-Heikkilä, S.(2023). The Riddle of How Fisheries Influence Genetic Diversity. Fishes 2023, 8, 510. 10.3390/fishes8100510

Salerno Jonathan, Jacob Mwalyoyo, Tim Caro, Emily Fitzherbert, and Monique Borgerhoff Mulder (2017). The Consequences of Internal Migration in Sub-Saharan Africa: A Case Study

Seehausen, O (2002). Patterns in fish radiation are compatible with the Pleistocene desiccation of Lake Victoria and the 14600-year history of its cichlid species flock

Therkildsen, N.O.; Nielsen, E.E.; Swain, D.P.; Pedersen, J.S.(2010) Large effective population size and temporal genetic stability in Atlantic cod (Gadus morhua) in the southern Gulf of St. Lawrence. Canadian Journal of Fisheries and Aquatic Sciences, 2010, 67, 1585–1595.

Tibihika, P. D., Curto, M. A., Negash, E., Waidbacher, H., Masembe, C., Akoll, P., Meimberg, H., (2020.) Molecular genetic diversity and differentiation of Nile tilapia (Oreochromis niloticus, L. 1758) in East African natural and stocked populations. Evolutionary Biology, 20(16), 1-20. DOI: 10.21203/rs.2.11849/v4

Trewavas, E. 1983. Tilapiine fishes of the Genera Sarotherodon,Oreochromis, and Danakilia. British Museum (Natural History), London; Timm, L.E. A fair fight between molecular marker types in a seascape genetics setting. Mol. Ecol. 2020, 29, 2133–2136.

Therkildsen, N.O.; Wilder, A.P.; Conover, D.O.; Munch, S.B.; Baumann, H.; Palumbi, S.R. Contrasting genomic shifts underlie parallel phenotypic evolution in response to fishing. Science (2019), 365, 487–490.

Todesco M, Pascual MA, Owens GL, Ostevik KL, Moyers BT, Hübner S, et al. Hybridization and extinction. Evol Appl. 2016;9(7):892–908

Twesigye C.K. Nsubuga F. W., Raja, R. Kato, P. (2024). Effects of Oil Exploration on Wildlife Resources in Murchison-Semliki Landscape. Journal of Environment and Earth Science ISSN 2224-3216. ISSN 2225-0948 (Online).Vol.14, No.3, 2024. DOI: 10.7176/JEES/14-3-02

Twesigye, C.K. S. Onywere, Z. Getenga, S. Mwakalila, J.Nakiranda (2011). The Impact of Land Use Activities on Vegetation Cover and Water Quality in the Lake Victoria Watershed. The Open Environmental Engineering Journal ISSN 1874- 8295 Volume 4(1-12).

Twesigye, C.K and Byarugaba, W. (2009).Population genetics of the Nile tilapia(Oreochromis niloticus) from Native and introduced populations of the Albertine Rift and the Lake Victoria Basin, East Africa. Uganda Journal.

Welcomme, R., Cowx IG, Coates D, Béné C, Funge-Smith S, Halls A, et al.(2010). Inland capture fisheries. Philosophical Transactions of the Royal Society B: Biological Sciences.2010;365(1554):2881–96.

Witte, F., van Oijen, M.J.P. and Sibbing, F.A. (2009). ‘Fish Fauna of the Nile’. In: H.J. Dumont (ed.)The Nile: Origin, Environments, Limnology and Human Uses. Monographiae Biologicae. pp. 647–675. Dordrecht, Netherlands: Springer Netherlands.




How to Cite

Twesigye Kakuhikire, C., Nsubuga, F. W., Raja, R., & Kato, P. (2024). Genetic diversity of Nile tilapia (Oreochromis niloticus, L. 1758) in native and introduced populations in East Africa. Journal of Wildlife and Biodiversity, 8(3), 296–312.